Other than the empty hole, there isn't any real risk not having that bolt there (if the well nut is missing or broken off). You may get some rattle or minor movement in the panel, but it's not going to fall off the bike.
We should point out that in addition to the 3 bolts you can see holding the panel, there's a plastic push rivet at the top, facing the backside of the windscreen (visible if you look thru the windscreen). It's possible to remove it with the windscreen on, but easier with it off (especially if you haven't done it before). Personally, I don't have those push rivets on the bike anymore, just so I don't have to mess with them.